Variant report

Variant	rs2280718
Chromosome Location	chr2:54587596-54587597
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54578951..54582305-chr2:54585861..54589772,4	K562	blood:
2	chr2:54587411..54590325-chr2:54591088..54593008,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10165083	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10182366	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10201089	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10865282	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12617259	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1405832	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1405833	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1527649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2280721	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3813463	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4459768	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4567978	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4606970	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6748355	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6751866	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7566809	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7566819	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7584922	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941351	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs941352	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv532512	chr2:54453210-54630755	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1004632	chr2:54469283-54590480	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2280718	ACYP2	cis	parietal	SCAN
rs2280718	C2orf73	cis	Thyroid	GTEx
rs2280718	PSME4	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54586200-54590600	Enhancers	Fetal Heart	heart
2	chr2:54586400-54587600	Enhancers	Left Ventricle	heart
3	chr2:54586400-54587800	Enhancers	Fetal Muscle Leg	muscle
4	chr2:54586400-54588200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr2:54586800-54587800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:54587000-54587600	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr2:54587000-54587600	Flanking Active TSS	NHDF-Ad	bronchial
8	chr2:54587000-54587800	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr2:54587000-54587800	Active TSS	Brain Anterior Caudate	brain
10	chr2:54587200-54587600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:54587200-54587600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:54587200-54587600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:54587200-54587600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
14	chr2:54587200-54587600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:54587200-54587600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:54587200-54587600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:54587200-54587600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:54587200-54587600	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr2:54587200-54587600	Enhancers	Liver	Liver
20	chr2:54587200-54587600	Flanking Active TSS	Brain Angular Gyrus	brain
21	chr2:54587200-54587600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:54587200-54587600	Enhancers	Fetal Kidney	kidney
23	chr2:54587200-54587600	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr2:54587200-54587600	Flanking Active TSS	Fetal Lung	lung
25	chr2:54587200-54587600	Flanking Active TSS	Ovary	ovary
26	chr2:54587200-54587600	Enhancers	Pancreas	Pancrea
27	chr2:54587200-54587600	Active TSS	Rectal Smooth Muscle	rectum
28	chr2:54587200-54587600	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr2:54587200-54587600	Flanking Active TSS	HepG2	liver
30	chr2:54587200-54587600	Flanking Active TSS	HUVEC	blood vessel
31	chr2:54587200-54587600	Enhancers	NHEK	skin
32	chr2:54587200-54587800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:54587200-54587800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:54587200-54587800	Flanking Active TSS	Brain Hippocampus Middle	brain
35	chr2:54587200-54587800	Active TSS	Colon Smooth Muscle	Colon
36	chr2:54587200-54587800	Active TSS	Stomach Smooth Muscle	stomach
37	chr2:54587200-54587800	Flanking Active TSS	NH-A	brain
38	chr2:54587200-54587800	Active TSS	Osteobl	bone
39	chr2:54587200-54588000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:54587400-54587600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:54587400-54587600	Active TSS	Brain Cingulate Gyrus	brain
42	chr2:54587400-54587600	Active TSS	Brain Substantia Nigra	brain
43	chr2:54587400-54587600	Flanking Active TSS	Fetal Brain Male	brain
44	chr2:54587400-54587600	Flanking Active TSS	HSMMtube	muscle
45	chr2:54587400-54587800	Active TSS	Right Atrium	heart
46	chr2:54587400-54587800	Flanking Active TSS	NHLF	lung
47	chr2:54587400-54589200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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